Heba Morayef, a researcher with the group, said some Egyptians are expressing concern that the two most divisive candidates garnered enough votes to participate in the run-off vote.

“[You saw] noticeably low voter turnout than the first round of presidential election. The various monitoring organizations -- both Egyptian and international -- have noted that as well,” said Morayef.

“Just comparing, the queues a much shorter this time, and I think it was because less people feel motivated to choose between the two (most) divisive candidates compared to the first round when there were 13 candidates.”

The official outcome of the winner of Egypt's first freely elected president is scheduled to be announced Thursday, but unofficial results are expected earlier in the week.

The voters have a choice between a Mubarak era candidate, former Prime Minister Ahmed Shafiq, and an Islamist, the Muslim Brotherhood candidate Mohammed Morsi.

Analysts say the country could remain divided if the winner fails to unite the people behind him.

“That would be a difficult and probably an impossible task…and definitely in the short term, we’ve just had several weeks where campaigning around the presidential elections have been primarily one of seeking to discredit the opposing candidate,” said Morayef.

“This was a very divisive round-off because on each side people fear the other candidate -- fear because there have been accusations of using violence, of using thugs, and trying to kill protesters of both sides. So this is happening in a climate where there is a lack of a sense of security about the future and lack of trust in each of the opposing candidates.”

Morayef said the new president faces the challenge of not knowing the powers available to work with since, she said, there is now neither a constitution nor a parliament.

She adds that the new president will have legitimacy that the military, which has ruled the country since the ouster of former President Hosni Mubarak, did not have.

“The question becomes what negotiations [the winner] will have with the military and what deals they will strike with the military in terms of the powers of the new president,” said Morayef.

“There have been negotiations over the past few days because the military is planning to announce an annex to the constitutional declaration in which it plans to spell out the powers of the new president. It has already said it will retain legislative powers, and it will retain control over the state budget.”